gentree: apply patches on by one

Instead of trying to infer the directory structure, which
was only used for verbose output and the git debug option,
just apply the patches on by one in the correct order.

Also warn if finding a .patch file that doesn't contain a
patch, just in case the patch library doesn't understand
some patches properly, for debugging purposes mostly.

Signed-off-by: Johannes Berg <johannes.berg@intel.com>

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